PSORT Bibliography

Please cite the following reference when you make use of the result of this server:

(standard reference for PSORT/PSORT II)

Nakai, K. and Horton, P., PSORT: a program for detecting the sorting signals of proteins and predicting their subcellular localization, Trends Biochem. Sci, 24(1) 34-35 (1999).
(PubMed)

(for eukaryotic data)

Nakai, K. and Kanehisa, M., A knowledge base for predicting protein localization sites in eukaryotic cells, Genomics 14, 897-911 (1992).
(PubMed)

(for prokaryotic data)

Nakai, K. and Kanehisa, M., Expert system for predicting protein localization sites in Gram-negative bacteria, PROTEINS: Structure, Function, and Genetics 11, 95-110 (1991).
(PubMed)

(analysis of yeast chromosome III ORFs)

Goffeau, A., Nakai, K., Slonimski, P., and Risler, J.-L., The membrane proteins encoded by yeast chromosome III genes, FEBS Lett. 325, 112-117 (1993).
(PubMed)

Goffeau, A., Slonimski, P., Nakai, K., and Risler, J.L., How many yeast genes code for membrane-spanning proteins?, Yeast 9, 691-702 (1993).
(PubMed)

(for reviews on protein sorting and related areas)

Horton, P., Mukai, Y., and Nakai, K., Chapter 14: Protein subcelular localization prediction, in L. Wong (ed.), Practical Bioinformatician, World Scientific Publishing Co., pp.193-216 (2004)

Nakai, K. Chapter 14: Signal peptides, in Ulo Langel (ed.), Cell-Penetrating Peptides: Processes and Applications, 295-324, CRC Press (2002).

Nakai, K., Prediction of in vivo fates of proteins in the era of genomics and proteomics, J. Struct. Biol., 134(2/3), 103-116 (2001).
(PubMed)

Kenta Nakai, Protein sorting signals and prediction of subcellular localization, Adv. Protein Chem. 54, 277-344 (2000).
(PubMed)

Kenta Nakai, Predicting various targeting signals in amino acid sequences, Bull. Inst. Chem. Res., Kyoto Univ. 69, 269-291 (1991).
(Click here to get more information)

(for our attempt to improve the reasoning algorithm of PSORT)

Horton, P. and Nakai, K., A probabilistic classification system for predicting the cellular localization sites of proteins, Intellig. Syst. Mol. Biol. 4, 109-115 (1996).
(PubMed)

Horton, P. and Nakai, K., Better prediction of protein cellular localization sites with the k nearest neighbor classifier, Intellig. Syst. Mol. Biol. 5, 147-152 (1997).
(PubMed)

(for our attempt to improve the PSORT subprograms)

Nakai, K., Refinement of the prediction methods of signal peptides for the genome analyses of Saccharomyces cerevisiae and Bacillus subtilis, Genome Informatics Workshop GIW-96,72-81 (1996).
(Click here to get more information)

Fujiwara, Y., Asogawa, M., and Nakai, K., Prediction of mitochondrial targeting signals using hidden Markov models, Genome Informatics Workshop, 53-60, (1997).
(PubMed)

(for iPSORT and PSORT-B)

Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S., Extensive feature detection of N-terminal protein sorting signals, Bioinformatics 18(2), 298-305 (2002).
(PubMed)

Gardy, J. L., Spencer, C., Wang, K., Ester, M., Tusnady, G. E., Simon, I, Hua, S., deFays, K., Lambert, C., Nakai, K. and Brinkman, F. S., PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria, Nucl. Acids Res. 31(13), 3613-3617 (2003).
(PubMed)